Bio::Tools::Run::PiseApplication::dotmatcher.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

Bio::Tools::Run::PiseApplication::dotmatcher

SYNOPSIS

   #

DESCRIPTION

Bio::Tools::Run::PiseApplication::dotmatcher 
       Bioperl class for:
 
         DOTMATCHER      Displays a thresholded dotplot of two sequences (EMBOSS)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/dotmatcher.html 
          for available values):
 
 
                 dotmatcher (String)
 
                 init (String)
 
                 sequencea (Sequence)
                         sequencea -- any [single sequence] (-sequencea)
                         pipe: seqfile
 
                 sequenceb (Sequence)
                         sequenceb [single sequence] (-sequenceb)
 
                 windowsize (Integer)
                         window size over which to test threshhold (-windowsize)
 
                 threshold (Integer)
                         threshold (-threshold)
 
                 matrixfile (Excl)
                         Matrix file (-matrixfile)
 
                 stretch (Switch)
                         Stretch plot (-stretch)
 
                 data (Switch)
                         Display as data (-data)
 
                 graph (Excl)
                         graph [device to be displayed on] (-graph)
 
                 xygraph (Excl)
                         xygraph (-xygraph)
 
                 outfile (OutFile)
                         Display as data (-outfile)
 
                 auto (String)
 
                 psouput (String)

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. 
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: 
   http://bugzilla.open-bio.org/

AUTHOR

Catherine Letondal (letondal@pasteur.fr) Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided ``as is'' without warranty of any kind.

SEE ALSO

•
http://bioweb.pasteur.fr/seqanal/interfaces/dotmatcher.html
•
Bio::Tools::Run::PiseApplication
•
Bio::Tools::Run::AnalysisFactory::Pise
•
Bio::Tools::Run::PiseJob

new

  Title   : new()
  Usage   : my $dotmatcher = Bio::Tools::Run::PiseApplication::dotmatcher->new($location, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::dotmatcher object.
            This method should not be used directly, but rather by 
            a Bio::Tools::Run::AnalysisFactory::Pise instance.
            my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
            my $dotmatcher = $factory->program('dotmatcher');
  Example : -
  Returns : An instance of Bio::Tools::Run::PiseApplication::dotmatcher.